Michael:
I disagree on a couple of points - the primary one being your suggestion that the data 'crossover' was a display-only problem.
The issue of whether the contacts were linked to the correct customers is a secondary one, and may well be a display problem. However, the primary issue was that the contact information - specifically their names, email address, and phone numbers - overwrote existing information in the Employee tables, which then was propogated to our QuickBooks database during a synch. Literally, "Tom" became "Joyce", his phone and email were replaced by hers... and any report of his sales transactions run in QuickBooks reported that fact.
I'm quite sure that during the import/exports that I was performing to update our data, at no time did I change the Employee name to that of the stray contact. There'd be no reason to do so, obviously.
Denise corrected the *names* in the QB Employee file that we believe were introduced by the Method synch. Subsequent synchs show that the Employee name fixes are "holding." However, she also fixed the email addresses, but those were overridden by the next synch, as the Method data was still incorrect.
With the MI engine disconnected and turned off, I have now exported, fixed, and re-imported the Employee file. I have also made changes to the SalesRepLookup table (unrelated to the current issues), and am now re-importing these changes.
When those are done, I'll run Customers and Transactions Updates (all records), resynch, and we'll see where we are.